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- PDB-1fnn: CRYSTAL STRUCTURE OF CDC6P FROM PYROBACULUM AEROPHILUM -

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Basic information

Entry
Database: PDB / ID: 1fnn
TitleCRYSTAL STRUCTURE OF CDC6P FROM PYROBACULUM AEROPHILUM
ComponentsCELL DIVISION CONTROL PROTEIN 6
KeywordsCELL CYCLE / cdc6 / cdc18 / orc1 / AAA protein / DNA replication initation factor / cell cycle control factor
Function / homology
Function and homology information


DNA replication origin binding / DNA replication / cell division / ATP binding
Similarity search - Function
Orc1/Cdc6-type DNA replication protein, archaea / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / AAA domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Orc1/Cdc6-type DNA replication protein, archaea / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / AAA domain / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ORC1-type DNA replication protein
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLiu, J. / Smith, C.L. / DeRyckere, D. / DeAngelis, K. / Martin, G.S. / Berger, J.M.
CitationJournal: Mol.Cell / Year: 2000
Title: Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control.
Authors: Liu, J. / Smith, C.L. / DeRyckere, D. / DeAngelis, K. / Martin, G.S. / Berger, J.M.
History
DepositionAug 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION CONTROL PROTEIN 6
B: CELL DIVISION CONTROL PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,4296
Polymers88,5262
Non-polymers9034
Water5,891327
1
A: CELL DIVISION CONTROL PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7143
Polymers44,2631
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CELL DIVISION CONTROL PROTEIN 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7143
Polymers44,2631
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.070, 132.070, 82.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein CELL DIVISION CONTROL PROTEIN 6 / CDC6P


Mass: 44262.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Plasmid: PLASMID PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZYK1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.67 Å3/Da / Density % sol: 73.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 mM Cacodylate pH 6.5, 100 mM NaCl, 20 mM Mg (OAc)2, 6 % MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %MPD1reservoir
240 mMmagnesium acetate1reservoir
320 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9611
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9611 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 106577 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 34 Å2 / Rsym value: 0.057 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.077 Å / Redundancy: 2.5 % / Rsym value: 0.285 / % possible all: 98.7
Reflection
*PLUS
Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.285

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Processing

Software
NameClassification
SOLVEphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 8852 8 %RANDOM
Rwork0.221 ---
all-99247 --
obs-97721 98.4 %-
Displacement parametersBiso mean: 46.13 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6088 0 56 338 6482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d1.9
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9

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